Images in standard WordPress photo galleries are not identified as in use and therefore are assigned to the deletion list. This is with WP 3.6.1 and plugin v1.6.0.
The gallery code is standard:
[gallery columns="5" link="file" ids="1303,1304,1305,1306,1307,1308,1309,1310,1311,1350,1351,1352,1364,1365,1366,1367,1368,1369,1370,1371,1372,1373,1374,1375,1376,1377"]
so it should be possible/easy to pick up the ids and determine that the images are in use.